Journal of microbiological methods最新文献

{"title":"Revelation of DNA aptamer sequences that bind Cyclospora cayetanensis","authors":"John G. Bruno","doi":"10.1016/j.mimet.2026.107410","DOIUrl":"10.1016/j.mimet.2026.107410","url":null,"abstract":"<div><div>This article completes the preliminary work published in the Journal of Fluorescence (PMID: 38109032) that demonstrated both external surface and seemingly internal binding of DNA aptamers to <em>Cyclospora cayetanensis</em> oocysts by disclosing the actual aptamer DNA sequences for public scrutiny and use in experimentation. These aptamer DNA sequences were previously held as trade secrets due to their perceived potential commercial value, but given the inability to generate much commercial interest in the aptamers for diagnostics applications, the author has decided to reveal the sequences so that other researchers may further study aptamer binding to the oocysts especially with regard to the unexpected internal binding. The author also shows that these aptamers appear useful in binding magnetic microbeads to the oocysts in buffer. Thus, perhaps the aptamers can be validated for magnetic separation of oocysts in more complex natural water or sewage samples as well. And finally, the public disclosure of these sequences could be applied to lateral flow test strip, Western blots and ELISA-like or other diagnostic assays. Both the refined and vetted list of highest affinity and most specific aptamer sequences against known <em>Cyclospora cayetanensis</em> proteins and whole oocysts as well as the comprehensive lists of thousands of aptamer sequences from next generation Illumina-based sequencing are disclosed.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107410"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146112785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A review on membrane biofouling during downtime of pharmaceutical water treatment equipment: Risks, mechanisms, and control strategies","authors":"Zijian Cui,&nbsp;Jun Ma,&nbsp;Yanjun Zhang,&nbsp;Zhenxing Song,&nbsp;Xinxi Xu","doi":"10.1016/j.mimet.2026.107415","DOIUrl":"10.1016/j.mimet.2026.107415","url":null,"abstract":"<div><div>Pharmaceutical water is a crucial component in drug manufacturing, as its quality directly affects drug safety and efficacy. This study focuses on membrane biofouling in pharmaceutical water systems during downtime, revealing its unique formation mechanisms: abrupt decreases in flow rate, reduced dissolved oxygen, and nutrient accumulation collectively create favourable conditions for microbial colonization. Biofilm formation not only causes a decline in membrane flux and an increase in transmembrane pressure but may also release harmful substances, such as endotoxins, posing a severe threat to water quality. The study systematically reviews existing control technologies, encompassing conventional methods such as chemical cleaning and backflushing, as well as innovative approaches including electrochemical treatment and cold atmospheric pressure plasma (CAP) technology. Furthermore, this paper prospectively explores future research directions, such as the development of green antifouling agents and the application of intelligent monitoring technologies, providing a scientific basis and technical support for achieving water safety and sustainable development in the pharmaceutical industry.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107415"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146119334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Usefulness of approved and newly emerging non-cultural assays for early detection of invasive fungal infections in pediatric patients: A scoping review","authors":"Jarom Kuhre ,&nbsp;Manav Jain ,&nbsp;Sheri Hohmann ,&nbsp;Elena Y. Enioutina","doi":"10.1016/j.mimet.2026.107389","DOIUrl":"10.1016/j.mimet.2026.107389","url":null,"abstract":"<div><h3>Introduction and objective</h3><div>Invasive fungal infections (IFI) affect millions worldwide, especially the immunocompromised and pediatric patients. The standard fungal culture has low sensitivity and is slow for fungal identification. Rapid and accurate laboratory assays may support early successful treatment. Although the European Organization for Research and Treatment of Cancer/Mycoses Study Group Education and Research Consortium (EORTC/MSGERC) has proposed IFI diagnostic criteria, there are few recommendations for children. This scoping review analyzed the sensitivity, specificity, and positive and negative predictive value of standard and recently developed non-cultural laboratory assays to diagnose IFI in children.</div></div><div><h3>Methods</h3><div>PubMed, Embase, Scopus, and Web of Science were searched from January 1, 2016, to March 23, 2025, for free, full-text publications for pediatric IFI and the EORTC/MSGERC-recommended fungal antigen assays (1,3)-ß-D-glucan and galactomannan. The same databases were searched for articles published before January 30, 2025, for emerging assays, Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), T2Candida, and lateral flow immunoassays (LFA).</div></div><div><h3>Results</h3><div>From the fungal antigen studies reviewed, (1,3)-ß-D-glucan and galactomannan assays exhibit varying rates of sensitivity and specificity, poor positive predictive value, and high negative predictive value. From the emerging assay studies, MALDI-TOF MS had near 100% sensitivity, T2Candida reported high specificity, and only one article reviewed LFA.</div></div><div><h3>Conclusion</h3><div>Despite varying accuracy and reliability, the fungal antigen assays offer the benefits of speed, noninvasive collection, and serial testing. The emerging assays appear faster and more sensitive, but few outcomes were reported. This limits comparisons between emerging laboratory assays and fungal culture.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107389"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145989617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An efficient targeted gene deletion approach for Trichoderma atroviride using Agrobacterium tumefaciens-mediated transformation","authors":"Mengke Li ,&nbsp;Yihong Li ,&nbsp;Xiaoyu Zhang,&nbsp;Hui Zhou,&nbsp;Yusheng Liu,&nbsp;Qiuye Liu,&nbsp;Shuqin Xiao","doi":"10.1016/j.mimet.2026.107407","DOIUrl":"10.1016/j.mimet.2026.107407","url":null,"abstract":"<div><div><em>Trichoderma atroviride</em> is well-known biocontrol fungus that plays a crucial role in controlling plant fungal diseases. In this study, the Serine Protease (<em>T. atSp1</em>) gene of <em>T. atroviride</em> was selected as the target gene to investigate the effects of <em>Agrobacterium tumefaciens</em> concentration, conidial concentration, mixing ratio of conidia and <em>Agrobacterium</em> cells, and induction time on transformation efficiency. The optimal knockout system was achieved under conditions that the density of <em>A. tumefaciens</em> was OD₆₀₀ = 0.5, the concentration of conidia suspension was 10⁶ conidia/mL, the mixture ratio of conidia suspension and <em>A. tumefaciens</em> AGL-1 was 1:1, and the induction time was 0.5 h. The transformation efficiency reached 28.33 to 61.67 transformants per 10⁶ conidia under the optimized conditions. The Δ<em>T. atSp1</em> was successfully validated by PCR analysis. Additionally, two genes of <em>T. atEDG1</em> and <em>T. atchi18</em> were also knocked out and verified, further demonstrating the robustness of this ATMT system. This study provides a stable and efficient genetic manipulation protocol for <em>T. atroviride</em>, facilitating further to understand genes function and biocontrol mechanisms.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107407"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146044254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ciliates as next-generation bioindicators in pollution-impacted freshwaters: Integrating community signatures with stress-response endpoints","authors":"Sandeep Antil ,&nbsp;Govindhasamay R. Varatharajan ,&nbsp;Jean Claude Ndayishimiye ,&nbsp;Pascaline Nyirabuhoro ,&nbsp;Damir Saldaev ,&nbsp;Santosh Kumar ,&nbsp;Ravi Toteja ,&nbsp;Seema Makhija ,&nbsp;Antonietta La Terza ,&nbsp;Yuri A. Mazei","doi":"10.1016/j.mimet.2026.107412","DOIUrl":"10.1016/j.mimet.2026.107412","url":null,"abstract":"<div><div>Aquatic ecosystems are increasingly threatened by diverse pollutants that compromise ecological integrity and impair ecosystem functioning. Conventional physicochemical monitoring methods are insufficient to detect early biological responses or cumulative stress. Bioindicators offer a biologically integrative, cost-effective, and ecologically meaningful alternative. This review synthesizes current knowledge on established and emerging bioindicator groups, with a critical appraisal of ciliates (Phylum Ciliophora), whose short generation times, trophic versatility, and suitability for both morphological and molecular assays position them as promising next-generation indicators of freshwater ecosystem health. We identify a clear research gap: although numerous primary studies document dose-dependent cytotoxic, oxidative-stress, and behavioural responses in ciliates, but no comprehensive review has consolidated these findings or outlined how ciliates can be operationalized in biomonitoring frameworks. The objectives of this review are to (i) compile and evaluate ciliate-based assays ranging from microscopy to qRT-PCR and multi-omics approaches, (ii) compare ciliates with other bioindicator taxa, and (iii) introduce a novel, empirically testable Ciliate Community Index (CCI) that integrates community composition, morphological integrity, and fold-change–based molecular biomarker responses into a single, unified assessment framework. Literature synthesis reveals consistent early-warning signals, such as motility impairment, vacuolization, and antioxidant responses, demonstrating the feasibility of multi-tiered monitoring while also underscoring the need for standardized protocols and field validation. We conclude that, with appropriate calibration and methodological harmonization, the CCI has strong potential to serve as a sensitive and scalable tool for assessing metal-impacted freshwater ecosystems.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107412"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146097179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The bacterial endotoxin test in the Chinese pharmacopoeia: A journey of international harmonization and national consideration","authors":"Tong Cai,&nbsp;Yusheng Pei","doi":"10.1016/j.mimet.2026.107411","DOIUrl":"10.1016/j.mimet.2026.107411","url":null,"abstract":"<div><div>The Bacterial Endotoxin Test (BET) is a critical quality control measure for parenteral drugs and sterile medical devices worldwide. As the global pharmaceutical industry becomes increasingly integrated, the harmonization of pharmacopoeial methods is an inevitable trend. The Chinese Pharmacopoeia (ChP), China's official national standard, has undergone significant evolution in its BET chapter, transitioning from initially referencing the United States Pharmacopoeia (USP) to progressively aligning with the International Council for Harmonization (ICH) Harmonized Tripartite Guideline:Evaluation and Recommendation of Pharmacopoeial Texts for Use in The ICH Regions on Bacterial Endotoxin Test General Chapter Q4B (ICH Q4B).</div><div>This article provides a comprehensive overview of the development of the BET in the ChP, with a special focus on the major revisions in the newly implemented 2025 edition. We detail how the ChP 2025 further converges with the ICH harmonized text in aspects such as method classification, procedural descriptions, and key validation parameters. Concurrently, we elucidate the scientific rationale for retaining specific “Chinese characteristics,” such as stricter requirements for water for BET, a different standard for average body weight in limit calculations, and more stringent retest protocols for the gel-clot method, all of which are rooted in domestic regulatory practices and public health considerations. Furthermore, we discuss China's proactive approach to addressing emerging global challenges like Low Endotoxin Recovery (LER) and its pioneering research into resource-saving micro-methods. This review aims to offer international stakeholders a clear perspective on the scientific rigor, commitment to global standards, and unique risk-based considerations that define the modern BET in China.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107411"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146080332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Automatic colony cell counting method of phytoplankton in microscopic images with multi-task learning","authors":"Renqing Jia ,&nbsp;Gaofang Yin ,&nbsp;Nanjing Zhao ,&nbsp;Min Zhang ,&nbsp;Chao Zhu ,&nbsp;Tianhong Liang ,&nbsp;Jingze Zhang ,&nbsp;Changbiao Yuan ,&nbsp;Jiamin Tao ,&nbsp;Peng Yun","doi":"10.1016/j.mimet.2026.107396","DOIUrl":"10.1016/j.mimet.2026.107396","url":null,"abstract":"<div><div>Phytoplankton are key bioindicators in aquatic ecosystems, where species distribution and cell abundance serve as vital metrics for environmental assessment. Although image-based automated identification has progressed, accurately counting colonial cells remains challenging. This paper proposes a novel method for simultaneous phytoplankton recognition and cell counting. Using ResNet50 as a backbone, deep features are extracted from microscopic images of algal colonies. These features are then fed into two parallel branches for classification and counting, respectively, with model parameters updated through alternating training. Evaluated on 16 common colonial algae species from Lake Chaohu, the proposed method achieved 99.2% identification accuracy, 93.9% average counting accuracy, with mean absolute error and mean squared error of 1.290 and 2.263, respectively. This method effectively overcomes the challenges associated with colonial phytoplankton by integrating both identification and counting into a unified framework, providing a robust tool for automated aquatic algal monitoring.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107396"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146029936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improved RNA extraction from Pseudomonas aeruginosa biofilms using a lysozyme-modified commercial kit","authors":"May M. Alrashed ,&nbsp;Abdurahman A. Niazy ,&nbsp;Rhodanne Nicole A. Lambarte ,&nbsp;Amani A. Niazy","doi":"10.1016/j.mimet.2026.107417","DOIUrl":"10.1016/j.mimet.2026.107417","url":null,"abstract":"<div><div>In this study, we modified the Zymo Research Quick-RNA™ Fungal/Bacterial Miniprep Kit for <em>P. aeruginosa</em> biofilms by incorporating a lysozyme pre-treatment step. The modified protocol markedly increased RNA yield with consistent purity compared to the manufacturer's protocols, meeting commonly accepted quality criteria for downstream molecular analyses. This modification offers a simple, reproducible improvement.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107417"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146119336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plant-based dyes as eco-friendly alternative for visualization of arbuscular mycorrhizal fungi","authors":"Bappa Karmakar,&nbsp;Mahasweta Chakraborty","doi":"10.1016/j.mimet.2026.107416","DOIUrl":"10.1016/j.mimet.2026.107416","url":null,"abstract":"<div><div>Synthetic dyes are traditionally used for staining arbuscular mycorrhizal fungi (AMF) yet their toxicity, environmental persistence raise health and ecological concerns. Herein, we report turmeric and pomegranate derived natural dyes for visualizing AMF which offer user-safe, low-cost, environmentally benign alternatives to synthetic stains, while promoting sustainable research practices.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107416"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146112742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"FastqOrienter: A Python utility for the automated orientation and quality diagnostics of paired-end Illumina metabarcoding reads","authors":"Daniele De Luca","doi":"10.1016/j.mimet.2026.107413","DOIUrl":"10.1016/j.mimet.2026.107413","url":null,"abstract":"<div><div>FastqOrienter is a Python tool that corrects inconsistent read orientations in Illumina paired-end metabarcoding reads using a primer-aware logic and IUPAC-compliant matching. In addition, it provides detailed diagnostics and actionable insights for discarded reads. It ensures data integrity for downstream pipelines like DADA2 and QIIME 2.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107413"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146100281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}